In 2071, roughly fifty years after an accident with a hyperspace gateway made the Earth almost uninhabitable, humanity has colonized most of the rocky planets and moons of the Solar System. Amid a rising crime rate, the Inter Solar System Police (ISSP) set up a legalized contract system, in which registered bounty hunters, also referred to as "Cowboys", chase criminals and bring them in alive in return for a reward.

Three decades after the great war between the humans and the Zentradi, the U.N. government is developing new technologies to use in their transforming fighter aircraft by running tests on the colony planet Eden. Military test pilots and former childhood friends, loose cannon Isamu Alva Dyson and the Zentradi mixed race Guld Goa Bowman, are selected to each pilot a new aircraft (Shinsei Industries' YF-19 & General Galaxy's YF-21) for Project Super Nova, to choose the newest successor to the VF-11 Thunderbolt variable fighter which is currently still in use by the U.N. Spacy military forces. Their own personal grudges end up disrupting the tests, and begin to wreak havoc on the program.